Hi, Thanks for the help, but my query doesn't seem to work.
Using the filter option from the Table Browser Page, I attempt to get the knownGenes table without all the splice variants listed by using the free-form query "name!=hg18.knownCanonical.transcript". However I get the following errors: --------------------------------------------------------------------------- Can't start query: select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds,proteinID,alignID from knownGene where chrom='chr19' and txStart<63811651 and txEnd>53014479 and (name!=knownCanonical.transcript) order by txStart --------------------------------------------------------------------------- --------------------------------------------------------------------------- mySQL error 1109: Unknown table 'knownCanonical' in where clause --------------------------------------------------------------------------- and --------------------------------------------------------------------------- Can't start query: select name,chrom,strand,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds,proteinID,alignID from knownGene where chrom='chr19' and txStart<63811651 and txEnd>53014479 and (name!=hg18.knownCanonical.transcript) order by txStart --------------------------------------------------------------------------- --------------------------------------------------------------------------- mySQL error 1109: Unknown table 'hg18.knownCanonical' in where clause --------------------------------------------------------------------------- Any ways to fix this? Thanks, Joses -----Original Message----- From: Kayla Smith [mailto:[email protected]] Sent: Fri 19-Dec-08 05:57 To: Joses HO Wei-Hao Cc: [email protected] Subject: Re: [Genome] Extracting exon lengths and coordinates from Table Browser Joses, Our hg18.knownCanonical table might be what you're looking for. This table describes the canonical splice variant of a gene. Please see this previously answered mailing list question: http://www.soe.ucsc.edu/pipermail/genome/2008-January/015274.html I hope this is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinoformatics Group Joses HO Wei-Hao wrote: > Hi, > > I have a genomic region of interest, and I want to extract all the exon > coordinates for sequence capture. The annotation database I want to use is > the UCSC Known Genes database. > > However, it seems to me that the Known Genes database contains splice > variants for several genes. I just want the start and stop coordinates of all > exons (both coding and non-coding, and both known and novel) within my region > of interest, without any duplicated exons. Any idea on how this can be done? > > Thanks, > Joses > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
